rs1509729

Positions:

• chr11-109056756-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.309 in 151,954 control chromosomes in the GnomAD database, including 7,400 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46955 AN: 151836 Hom.: 7379 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.316

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.309 AC: 47010 AN: 151954 Hom.: 7400 Cov.: 32 AF XY: 0.313 AC XY: 23204 AN XY: 74234

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.310

Alfa AF: 0.296 Hom.: 9041

Bravo AF: 0.310

Asia WGS AF: 0.272 AC: 947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	10
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1509729; hg19: chr11-108927483;